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<a href="MatrixScorer_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    Commercial users should ask about our dual licensing model.</span>
<a name="l00020"></a>00020 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00021"></a>00021 <span class="comment">*/</span>
<a name="l00022"></a>00022 
<a name="l00028"></a>00028 <span class="preprocessor">#ifndef MOLTK_ALIGN_MATRIX_SCORER_H</span>
<a name="l00029"></a>00029 <span class="preprocessor"></span><span class="preprocessor">#define MOLTK_ALIGN_MATRIX_SCORER_H</span>
<a name="l00030"></a>00030 <span class="preprocessor"></span>
<a name="l00031"></a>00031 <span class="preprocessor">#include &quot;<a class="code" href="DPPosition_8hpp.html" title="Templated classes GapScore and DPPosition to efficiently represent sequence residues during alignment...">moltk/DPPosition.hpp</a>&quot;</span>
<a name="l00032"></a>00032 <span class="preprocessor">#include &quot;<a class="code" href="Alignment_8hpp.html" title="Alignment class representing a sequence alignment.">moltk/Alignment.hpp</a>&quot;</span>
<a name="l00033"></a>00033 <span class="preprocessor">#include &quot;<a class="code" href="SubstitutionMatrix_8hpp.html" title="SubstitutionMatrix class for look up of residue alignment scores.">moltk/SubstitutionMatrix.hpp</a>&quot;</span>
<a name="l00034"></a>00034 
<a name="l00035"></a>00035 <span class="keyword">namespace </span>moltk {
<a name="l00036"></a>00036 
<a name="l00041"></a>00041 <span class="keyword">template</span>&lt;<span class="keyword">class</span> SCORE_TYPE, <span class="keywordtype">int</span> GAP_NSEGS&gt;
<a name="l00042"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html">00042</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1MatrixScorer__.html" title="MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250.">MatrixScorer_</a>
<a name="l00043"></a>00043 {
<a name="l00044"></a>00044 <span class="keyword">public</span>:
<a name="l00046"></a>00046     <span class="keyword">explicit</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html#a093911098a3e0b7ad665a0cf2a5c6447" title="Create a MatrixScorer using a particular substitution matrix.">MatrixScorer_</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1SubstitutionMatrix__.html" title="SubstitutionMatrix scores alignments using a residue type matrix such as BLOSUM62 or PAM250...">moltk::SubstitutionMatrix_&lt;SCORE_TYPE&gt;</a>&amp; <a class="code" href="classmoltk_1_1MatrixScorer__.html#a4bf1242ff86ad47455d09ce4df1a18e7">matrix</a>);
<a name="l00048"></a>00048     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html#a08105eea98536c8b5766d1b2f6a9b145" title="Create precached data structures for alignment of two individual sequences.">create_positions</a>(
<a name="l00049"></a>00049         std::vector&lt;<a class="code" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__UNGAPPED__SEQUENCES_00_01GAP__NSEGS_01_4.html" title="Specialization of alignment column cache for alignment two individual sequences.">dp::DPPosition&lt;SCORE_TYPE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, GAP_NSEGS&gt;</a>*&gt;&amp; positions, 
<a name="l00050"></a>00050         <span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; alignment) <span class="keyword">const</span>;
<a name="l00052"></a>00052     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html#a08105eea98536c8b5766d1b2f6a9b145" title="Create precached data structures for alignment of two individual sequences.">create_positions</a>(
<a name="l00053"></a>00053         std::vector&lt;<a class="code" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__GAPPED__ALIGNMENTS_00_01GAP__NSEGS_01_4.html" title="Specialization of alignment column cache for alignment of alignments.">dp::DPPosition&lt;SCORE_TYPE, dp::DP_ALIGN_GAPPED_ALIGNMENTS, GAP_NSEGS&gt;</a>*&gt;&amp; positions, 
<a name="l00054"></a>00054         <span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; alignment) <span class="keyword">const</span>;
<a name="l00055"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html#a0d7def4e72c6e4263cb9506a1055978b">00055</a>     <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html#a0d7def4e72c6e4263cb9506a1055978b">get_end_gaps_free</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html#a69dc9913654f395b8a6912cd5866edc7">b_end_gaps_free</a>;}
<a name="l00056"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html#abe3caf1c15a2e325c7bd942b38fa8295">00056</a>     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html#abe3caf1c15a2e325c7bd942b38fa8295">set_end_gaps_free</a>(<span class="keywordtype">bool</span> f) {<a class="code" href="classmoltk_1_1MatrixScorer__.html#a69dc9913654f395b8a6912cd5866edc7">b_end_gaps_free</a> = f;}
<a name="l00058"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html#a74e1d7a6961120ce14f0097b88907514">00058</a>     SCORE_TYPE <a class="code" href="classmoltk_1_1MatrixScorer__.html#a74e1d7a6961120ce14f0097b88907514" title="Alignment score reduction for initiating an alignment gap.">get_default_gap_open_score</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html#aa6e2fb51837602663ca39a4ba1b9fa3f">default_gap_open_score</a>;}
<a name="l00060"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html#a6dce77af635e8e89b12eb632f88371f2">00060</a>     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html#a6dce77af635e8e89b12eb632f88371f2" title="Set alignment score reduction for initiating an alignment gap.">set_default_gap_open_score</a>(SCORE_TYPE <a class="code" href="classmoltk_1_1MatrixScorer__.html#ab90650541e6f63c72b6a20a1480b2de7" title="Look up score of two residue one-letter-codes in the matrix.">score</a>) {<a class="code" href="classmoltk_1_1MatrixScorer__.html#aa6e2fb51837602663ca39a4ba1b9fa3f">default_gap_open_score</a> = <a class="code" href="classmoltk_1_1MatrixScorer__.html#ab90650541e6f63c72b6a20a1480b2de7" title="Look up score of two residue one-letter-codes in the matrix.">score</a>;}
<a name="l00062"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html#ad4f161927c9c6f2491b345c24a120ac7">00062</a>     SCORE_TYPE <a class="code" href="classmoltk_1_1MatrixScorer__.html#ad4f161927c9c6f2491b345c24a120ac7" title="Alignment score reduction for increasing the length of an alignment gap by one position.">get_default_gap_extension_score</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html#ae46f2161ce2413aa901cfe80d79b4ac3">default_gap_extension_score</a>;}
<a name="l00064"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html#ae7fdb188444d50d14267783fd3bcba88">00064</a>     <span class="keywordtype">void</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html#ae7fdb188444d50d14267783fd3bcba88" title="Set Alignment score reduction for increasing the length of an alignment gap by one position...">set_default_gap_extension_score</a>(SCORE_TYPE <a class="code" href="classmoltk_1_1MatrixScorer__.html#ab90650541e6f63c72b6a20a1480b2de7" title="Look up score of two residue one-letter-codes in the matrix.">score</a>) {<a class="code" href="classmoltk_1_1MatrixScorer__.html#ae46f2161ce2413aa901cfe80d79b4ac3">default_gap_extension_score</a> = <a class="code" href="classmoltk_1_1MatrixScorer__.html#ab90650541e6f63c72b6a20a1480b2de7" title="Look up score of two residue one-letter-codes in the matrix.">score</a>;}
<a name="l00065"></a>00065 
<a name="l00067"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html#ab90650541e6f63c72b6a20a1480b2de7">00067</a>     SCORE_TYPE <a class="code" href="classmoltk_1_1MatrixScorer__.html#ab90650541e6f63c72b6a20a1480b2de7" title="Look up score of two residue one-letter-codes in the matrix.">score</a>(<span class="keywordtype">char</span> residue1, <span class="keywordtype">char</span> residue2)<span class="keyword"> const </span>{<span class="keywordflow">return</span> matrix.<a class="code" href="classmoltk_1_1SubstitutionMatrix__.html#a4eb58b41b9fef4021dd842b463d5d479" title="Look up score of two residue one-letter-codes in the matrix.">score</a>(residue1, residue2);}
<a name="l00069"></a>00069     SCORE_TYPE <a class="code" href="classmoltk_1_1MatrixScorer__.html#adbe9a587fd12d874ebe5edcdc9531d6d" title="Inefficient computation of sum-of-pairs score, for use in testing and debugging.">calc_explicit_sum_of_pairs_score</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_&lt;SCORE_TYPE&gt;</a>&amp; alignment) <span class="keyword">const</span>;
<a name="l00071"></a>00071     SCORE_TYPE <a class="code" href="classmoltk_1_1MatrixScorer__.html#a6369337ff8f5877031de76db62c2c3bf" title="Compute pair score between two sequences in an alignment.">calc_explicit_pair_score</a>(<span class="keywordtype">int</span> i, <span class="keywordtype">int</span> j, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_&lt;SCORE_TYPE&gt;</a>&amp; alignment) <span class="keyword">const</span>;
<a name="l00072"></a>00072 
<a name="l00073"></a>00073 <span class="keyword">protected</span>:
<a name="l00074"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html#a69dc9913654f395b8a6912cd5866edc7">00074</a>     <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html#a69dc9913654f395b8a6912cd5866edc7">b_end_gaps_free</a>;
<a name="l00075"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html#aa6e2fb51837602663ca39a4ba1b9fa3f">00075</a>     SCORE_TYPE <a class="code" href="classmoltk_1_1MatrixScorer__.html#aa6e2fb51837602663ca39a4ba1b9fa3f">default_gap_open_score</a>;
<a name="l00076"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html#ae46f2161ce2413aa901cfe80d79b4ac3">00076</a>     SCORE_TYPE <a class="code" href="classmoltk_1_1MatrixScorer__.html#ae46f2161ce2413aa901cfe80d79b4ac3">default_gap_extension_score</a>;
<a name="l00077"></a><a class="code" href="classmoltk_1_1MatrixScorer__.html#a4bf1242ff86ad47455d09ce4df1a18e7">00077</a>     <a class="code" href="classmoltk_1_1SubstitutionMatrix__.html" title="SubstitutionMatrix scores alignments using a residue type matrix such as BLOSUM62 or PAM250...">SubstitutionMatrix_&lt;SCORE_TYPE&gt;</a> <a class="code" href="classmoltk_1_1MatrixScorer__.html#a4bf1242ff86ad47455d09ce4df1a18e7">matrix</a>;
<a name="l00078"></a>00078 };
<a name="l00079"></a>00079 
<a name="l00080"></a><a class="code" href="namespacemoltk.html#a29b017023af90d3aa2eb917cfdbc59ac">00080</a> <span class="keyword">typedef</span> <a class="code" href="classmoltk_1_1MatrixScorer__.html">MatrixScorer_&lt;moltk::units::Information, 1&gt;</a> <a class="code" href="namespacemoltk.html#a29b017023af90d3aa2eb917cfdbc59ac">MatrixScorer</a>;
<a name="l00081"></a>00081 
<a name="l00082"></a>00082 } <span class="comment">// namespace moltk</span>
<a name="l00083"></a>00083 
<a name="l00084"></a>00084 <span class="preprocessor">#endif // MOLTK_ALIGN_MATRIX_SCORER_H</span>
<a name="l00085"></a>00085 <span class="preprocessor"></span>
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